Examples with XMLParser beast.util.XMLParser used on opensource projects

Example 31 with XMLParser

use of beast.util.XMLParser in project bacter by tgvaughan.

the class SimulatedACGTest method test5Taxon.

@Test
public void test5Taxon() throws Exception {
    Randomizer.setSeed(1);
    XMLParser parser = new XMLParser();
    beast.core.Runnable runnable = parser.parseFile(new File("examples/ACGsimulations/simulateACGs5taxon.xml"));
    runnable.run();
    List<Expectation> expectations = new ArrayList<>();
    expectations.add(new Expectation("acg.CFheight", 1.606, 1e-2));
    expectations.add(new Expectation("acg.CFlength", 4.181, 1e-2));
    expectations.add(new Expectation("acg.nConv", 21.0, 5e-2));
    LogAnalyser logAnalyser = new LogAnalyser("simulateACGs5taxon.stats", expectations);
    for (int i = 0; i < expectations.size(); i++) {
        assertTrue(expectations.get(i).isValid());
        assertTrue(expectations.get(i).isPassed());
    }
    Files.deleteIfExists(Paths.get("simulateACGs5taxon.stats"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxon.converted"));
    Files.deleteIfExists(Paths.get("simulateACGs5taxon.trees"));
}

Example 32 with XMLParser

use of beast.util.XMLParser in project bacter by tgvaughan.

the class CFConvSwapExperiment method main.

public static void main(String[] args) throws Exception {
    // Load model
    XMLParser parser = new XMLParser();
    MCMC mcmc = (MCMC) parser.parseFile(new File("inferencePreSimulatedData.xml"));
    State state = mcmc.startStateInput.get();
    state.setStateFileName("problem.state");
    state.restoreFromFile();
    double oldPosterior = state.robustlyCalcPosterior(mcmc.posteriorInput.get());
    ConversionGraph acg = (ConversionGraph) state.getStateNode(0);
    PrintStream ps = new PrintStream("proposal.trees");
    ps.println(acg);
    Node srcNode = acg.getNode(3);
    Node srcNodeS = getSibling(srcNode);
    Node destNode = acg.getNode(6);
    double t_srcNodeP = srcNode.getParent().getHeight();
    disconnectEdge(acg, srcNode);
    Locus locus = acg.getLoci().get(0);
    Conversion convToReplace = acg.getConversions(locus).get(27);
    acg.deleteConversion(convToReplace);
    Node srcNodeP = srcNode.getParent();
    connectEdge(acg, srcNode, destNode, convToReplace.getHeight2());
    // Move Conversions
    for (Conversion conv : acg.getConversions(locus)) {
        boolean moved = false;
        if (conv.getNode1() == srcNode && conv.getHeight1() > srcNodeP.getHeight()) {
            conv.setNode1(destNode);
            moved = true;
        }
        if (conv.getNode2() == srcNode && conv.getHeight2() > srcNodeP.getHeight()) {
            conv.setNode2(destNode);
            moved = true;
        }
        if (moved) {
            while (conv.getHeight1() > conv.getNode1().getParent().getHeight()) conv.setNode1(conv.getNode1().getParent());
            while (conv.getHeight2() > conv.getNode2().getParent().getHeight()) conv.setNode2(conv.getNode2().getParent());
        }
    }
    Conversion convNew = new Conversion();
    convNew.setLocus(locus);
    convNew.setStartSite(0);
    convNew.setEndSite(4000);
    convNew.setNode1(srcNode);
    convNew.setNode2(srcNodeS);
    convNew.setHeight1(convToReplace.getHeight1());
    convNew.setHeight2(t_srcNodeP);
    acg.addConversion(convNew);
    ps.println(acg);
    double newPosterior = state.robustlyCalcPosterior(mcmc.posteriorInput.get());
    System.out.println(newPosterior - oldPosterior);
// state.setStateFileName("proposal.state");
// state.storeToFile(1);
// Open state file
}

Example 33 with XMLParser

use of beast.util.XMLParser in project beast2 by CompEvol.

the class BeautiAlignmentProvider method getXMLData.

public static BEASTInterface getXMLData(File file) {
    String xml = "";
    try {
        // parse as BEAST 2 xml fragment
        XMLParser parser = new XMLParser();
        BufferedReader fin = new BufferedReader(new FileReader(file));
        while (fin.ready()) {
            xml += fin.readLine() + "\n";
        }
        fin.close();
        BEASTInterface runnable = parser.parseBareFragment(xml, false);
        BEASTInterface alignment = getAlignment(runnable);
        alignment.initAndValidate();
        return alignment;
    } catch (Exception ex) {
        // attempt to parse as BEAST 1 xml
        try {
            String ID = file.getName();
            ID = ID.substring(0, ID.lastIndexOf('.')).replaceAll("\\..*", "");
            BEASTInterface alignment = parseBeast1XML(ID, xml);
            if (alignment != null) {
                alignment.setID(file.getName().substring(0, file.getName().length() - 4).replaceAll("\\..*", ""));
            }
            return alignment;
        } catch (Exception ex2) {
            ex.printStackTrace();
            JOptionPane.showMessageDialog(null, "Loading of " + file.getName() + " failed: " + ex.getMessage() + "\n" + ex2.getMessage());
        }
        return null;
    }
}

Example 34 with XMLParser

use of beast.util.XMLParser in project beast2 by CompEvol.

the class BeautiConfig method initAndValidate.

@Override
public void initAndValidate() {
    parseSet(inlineInput.get(), null, inlineBEASTObject);
    parseSet(collapsedInput.get(), null, collapsedBEASTObjects);
    inlineBEASTObject.addAll(collapsedBEASTObjects);
    // parseSet(m_hidePanels.get(), "TAXON_SETS_PANEL,TIP_DATES_PANEL,PRIORS_PANEL,OPERATORS_PANEL", g_sHidePanels);
    parseSet(suppressInputs.get(), null, suppressBEASTObjects);
    parseSet(disableMenus.get(), null, disabledMenus);
    parseSet(disableButtons.get(), null, disabledButtons);
    parseMap(inputLabelMapInput.get(), inputLabelMap);
    parseMap(buttonLabelMapInput.get(), buttonLabelMap);
    // parseMap(m_editButtonStatus.get(), g_sEditButtonStatus);
    for (BeautiPanelConfig panel : panelsInput.get()) {
        panels.add(panel);
        // check for duplicates
        for (BeautiPanelConfig panel2 : panels) {
            if (panel2.nameInput.get().equals(panel.nameInput.get()) && panel2 != panel) {
                panels.remove(panels.size() - 1);
                break;
            }
        }
    }
    // InputEditor.setExpertMode(isExpertInput.get());
    subTemplates = subTemplatesInput.get();
    alignmentProvider = alignmentProviderInput.get();
    try {
        XMLParser parser = new XMLParser();
        hyperPriorTemplate = (BeautiSubTemplate) parser.parseBareFragment(HYPER_PRIOR_XML, true);
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 35 with XMLParser

use of beast.util.XMLParser in project beast2 by CompEvol.

the class BeastMCMC method parseArgs.

/**
 * parse command line arguments, and load file if specified
 * @throws IOException
 * @throws JSONException
 * @throws JSONParserException
 */
public void parseArgs(String[] args) throws IOException, XMLParserException, JSONException {
    int i = 0;
    boolean resume = false;
    boolean useStrictVersions = false;
    Map<String, String> parserDefinitions = new HashMap<>();
    File beastFile = null;
    try {
        while (i < args.length) {
            int old = i;
            if (i < args.length) {
                if (args[i].equals("")) {
                    i += 1;
                } else if (args[i].equals("-batch")) {
                    Logger.FILE_MODE = Logger.LogFileMode.only_new_or_exit;
                    i += 1;
                } else if (args[i].equals("-resume")) {
                    resume = true;
                    Logger.FILE_MODE = Logger.LogFileMode.resume;
                    System.setProperty("beast.resume", "true");
                    System.setProperty("beast.debug", "false");
                    i += 1;
                } else if (args[i].equals("-overwrite")) {
                    Logger.FILE_MODE = Logger.LogFileMode.overwrite;
                    i += 1;
                } else if (args[i].equals("-seed")) {
                    if (args[i + 1].equals("random")) {
                        m_nSeed = Randomizer.getSeed();
                    } else {
                        m_nSeed = Long.parseLong(args[i + 1]);
                    }
                    i += 2;
                } else if (args[i].equals("-threads")) {
                    m_nThreads = Integer.parseInt(args[i + 1]);
                    g_exec = Executors.newFixedThreadPool(m_nThreads);
                    i += 2;
                // use BEAST environment variable to set Beast directories as colon separated list
                // } else if (args[i].equals("-beastlib")) {
                // ClassDiscovery.setJarPath(args[i + 1]);
                // i += 2;
                } else if (args[i].equals("-prefix")) {
                    System.setProperty("file.name.prefix", args[i + 1].trim());
                    i += 2;
                } else if (args[i].equals("-D")) {
                    String[] strs = args[i + 1].split(",");
                    for (String str : strs) {
                        String[] strs2 = str.split("=");
                        if (strs2.length != 2) {
                            throw new IllegalArgumentException("Argument \"" + str + "\" is not well-formed: expecting name=value pairs");
                        }
                        String name = strs2[0];
                        String value = strs2[1];
                        parserDefinitions.put(name, value);
                    }
                    i += 2;
                } else if (args[i].equals("-strictversions")) {
                    useStrictVersions = true;
                    i += 1;
                }
                if (i == old) {
                    if (i == args.length - 1) {
                        beastFile = new File(args[i]);
                        i++;
                    } else {
                        throw new IllegalArgumentException("Wrong argument");
                    }
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new IllegalArgumentException("Error parsing command line arguments: " + Arrays.toString(args) + "\nArguments ignored\n\n" + getUsage());
    }
    if (beastFile == null) {
        // Not resuming so get starting options...
        List<String> MCMCargs = new ArrayList<>();
        Version version = new BEASTVersion2();
        String titleString = "<html><center><p>Bayesian Evolutionary Analysis Sampling Trees<br>" + "Version " + version.getVersionString() + ", " + version.getDateString() + "</p></center></html>";
        javax.swing.Icon icon = IconUtils.getIcon(BeastMain.class, "images/beast.png");
        String nameString = "BEAST " + version.getVersionString();
        BeastDialog dialog = new BeastDialog(new JFrame(), titleString, icon);
        if (!dialog.showDialog(nameString, m_nSeed)) {
            return;
        }
        switch(dialog.getLogginMode()) {
            case 0:
                /* do not ovewrite */
                break;
            case 1:
                MCMCargs.add("-overwrite");
                break;
            case 2:
                MCMCargs.add("-resume");
                break;
        }
        MCMCargs.add("-seed");
        MCMCargs.add(dialog.getSeed() + "");
        if (dialog.getThreadPoolSize() > 0) {
            MCMCargs.add("-threads");
            MCMCargs.add(dialog.getThreadPoolSize() + "");
        }
        boolean useBeagle = dialog.useBeagle();
        boolean beagleShowInfo = false;
        long beagleFlags = 0;
        if (useBeagle) {
            beagleShowInfo = dialog.showBeagleInfo();
            if (dialog.preferBeagleCPU()) {
                beagleFlags |= BeagleFlag.PROCESSOR_CPU.getMask();
            }
            if (dialog.preferBeagleSSE()) {
                beagleFlags |= BeagleFlag.VECTOR_SSE.getMask();
            }
            if (dialog.preferBeagleGPU()) {
                beagleFlags |= BeagleFlag.PROCESSOR_GPU.getMask();
            }
            if (dialog.preferBeagleDouble()) {
                beagleFlags |= BeagleFlag.PRECISION_DOUBLE.getMask();
            }
            if (dialog.preferBeagleSingle()) {
                beagleFlags |= BeagleFlag.PRECISION_SINGLE.getMask();
            }
        }
        if (beagleFlags != 0) {
            System.setProperty("beagle.preferred.flags", Long.toString(beagleFlags));
        }
        if (!useBeagle) {
            System.setProperty("java.only", "true");
        }
        File inputFile = dialog.getInputFile();
        if (!beagleShowInfo && inputFile == null) {
            System.err.println("No input file specified");
            System.exit(1);
        }
        MCMCargs.add(inputFile.getAbsolutePath());
        // BeastStartDialog dlg = new BeastStartDialog();
        // if (dlg.m_bOK) {
        // parseArgs(dlg.getArgs());
        // }
        parseArgs(MCMCargs.toArray(new String[0]));
        return;
    }
    Log.warning.println("File: " + beastFile.getName() + " seed: " + m_nSeed + " threads: " + m_nThreads);
    if (resume) {
        Log.info.println("Resuming from file");
    }
    if (useStrictVersions) {
        // grab "required" attribute from beast spec
        if (beastFile.getPath().toLowerCase().endsWith(".json")) {
            throw new IllegalArgumentException("The -strictversions flag is not implemented for JSON files yet (only XML files are supported).");
        } else {
            BufferedReader fin = new BufferedReader(new FileReader(beastFile));
            StringBuffer buf = new StringBuffer();
            String str = null;
            int lineCount = 0;
            while (fin.ready() && lineCount < 100) {
                str = fin.readLine();
                buf.append(str);
                buf.append(' ');
            }
            fin.close();
            str = buf.toString();
            int start = str.indexOf("required=");
            if (start < 0) {
                throw new IllegalArgumentException("Could not find a 'required' attribute in the XML. Add the required attribute, or run without the -strictversions flag");
            }
            char c = str.charAt(start + 9);
            start += 10;
            int end = str.indexOf(c, start);
            String packages = str.substring(start, end);
            PackageManager.loadExternalJars(packages);
        }
    } else {
        PackageManager.loadExternalJars();
    }
    // parse xml
    Randomizer.setSeed(m_nSeed);
    if (beastFile.getPath().toLowerCase().endsWith(".json")) {
        m_runnable = new JSONParser(parserDefinitions).parseFile(beastFile);
    } else {
        try {
            m_runnable = new XMLParser(parserDefinitions).parseFile(beastFile);
        } catch (SAXException | ParserConfigurationException e) {
            throw new IllegalArgumentException(e);
        }
    }
    m_runnable.setStateFile(beastFile.getName() + ".state", resume);
}